IRMPD technique

As mentioned earlier, CPMD simulations were carried out at 300K on deprotonated phosphorylated serine (p-ser-H) , and the resultant extracted spectrum correlates with the experimental IR spectrum obtained by the recently-developed InfraRed Multiple Photon Dissociation (IRMPD) technique, which was first described in this chapter in Volume 39. 

To determine the sites phosphorylation peptides are sequenced using CID-MS/MS, PSD, BCD, and IRMPD techniques. 

It is likely that theoretical methods, both ab initio and MD simulations, will be needed to resolve the complicated chemical decomposition of energetic materials. There are species and steps in the branching, sequential reactions that cannot be studied by extant experimental techniques. Even when experiments can provide some information it is often inferred or incomplete. The fate of methylene nitramine, a primary product observed by Zhao et al. [33] in their IRMPD/molecular beam experiments on RDX, is a prime example. Rice et al. [99, 100] performed extensive classical dynamics simulations of the unimolecular decomposition of methylene nitramine in an effort to help clarify its role in the mechanism for the gas-phase decomposition of RDX. 

J.W. Gauthier, T.R. Trautman, D.B. Jacobson, SORI for CID involving FT-ICR-MS. CID technique that emulates IRMPD, Anal. Chim. Acta, 246 (1991)211. 

Other fragmentation techniques have been introduced [108]. Some of these, e.g., sustained off-resonance irradiation (SORl) and infrared multiphoton dissociation (IRMPD), provide similar fragmentation as in CID, i.e., preferential backbone cleavages at the peptide amide bond (b- and y-ions). Others like electron-capture dissociation (ECD) [109-110] induce different fragmentation reactions, i.e., the formation of c- and z -ions due to cleavage of N-C bonds. 

Vibrational spectroscopy is an important probe used to determine the bonding and structural properties of molecules. Powerful techniques such as electron energy loss spectroscopy (EELS) have been developed, which allow one to obtain the vibrational properties of molecules chemisorbed upon surfaces. Due to low concentration, the highly reactive nature of the clusters, and the large number of possible species which are typically present in the cluster beams used to date, unconventional techniques are required in order to obtain spectroscopic information. One unconventional but powerful technique, infrared multiple photon dissociation (IRMPD), has recently been applied to the study of the vibrational properties of gas-phase metal clusters upon which one or more molecules have been chemisorbed. This same technique, IRMPD, has previously been used to obtain the vibrational spectra of ions, species for which it is difficult to apply conventional absorption techniques. 

In modem instrumentation, these techniques may both be applied to the same peptide to generate complementary sequence data and PTM data (IRMPD and ECD in FTICR MS,89 CID and ETD in QIT and LIT,90 and CID and ETD in QToF91). 

It is unusual for either CID or ETD to provide complete sequence information from any one peptide but the use of both techniques provides complementary information, which can gready extend the sequence coverage (Table 4). In addition, because the energy from the ETD process is directed into cleaving the Ca—N bond, the labile PTMs are preserved and their location in the peptide sequence can then be determined90 (see also discussion in Section 9.10.3.2.6 on the use of CID/IRMPD and ECD/ETD for protein/peptide sequencing, and Table 4). 

On the basis of the complementarity of CID/IRMPD and ECD/ETD, Zubarev et alul have concluded that de novo sequencing of peptides using these two fragmentation techniques in conjunction with high mass accuracy113,114 can be achieved with >95% reliability. They have furthermore stated that it is... 

Another ion activation method that is well suited for identification and sequence analysis of phosphopep-tides in the positive and negative polarity modes is infrared multiphoton dissociation (IRMPD).105,112 In this technique, phosphopeptides are irradiated with 10.6 pm photons emitted from a C02 laser. The phosphate group behaves like a chromophore for these photons, allowing evenly distributed cleavages in the peptide chain and more sequence coverage than the CID technique.105... 

Fragmentation of peptide and protein ions in FT-ICR mass spectrometry may be induced by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) [28], infrared multiphoton dissociation (IRMPD) [29,30], blackbody infrared radiative dissociation (BIRD) [31,32], surface-induced dissociation (SID) [33,34], and electron capture dissociation (ECD) [35,36]. These techniques are true MS/MS techniques in which the precursor ion is isolated prior to fragmentation. Additional techniques in which ions are not isolated but fragmented before they... 

IRMPD offers a number of advantages over SORI-CID. The principal advantage is that the introduction of gas to the ICR cell is obviated. There is no requirement for a pump-down delay, hence the speed of analysis is greater and the method is compatible with on-line separation techniques [61]. Unlike SORI-CID, blind-spots in the MS/MS spectrum do not occur because there is no resonant excitation of the product ions. All product ions are formed on-axis so there is no loss of resolution and it is possible to undertake further stages of MS/MS. A consequence of the on-axis position is the potential for secondary fragmentation, that is, the product ions can be photon activated also. Fragmentation of product ions can complicate spectral interpretation. 

Methods incorporating FT-ICR MS/MS have been applied also to bottom-up proteomic analyes. Hakansson et al. [66] applied ESI FT-ICR and IRMPD MS/MS to the analysis of glycoproteins isolated from human cerebrospinal fluid. Brock and co-workers [103] combined MALDI FT-ICR with SORI-CID. The throughput of this approach is hampered by the timescales associated with SORI-CID. Laskin and co-workers [104] compared approaches utilizing SORI-CID and SID coupled to ESI. The protein identification scores were comparable for the two techniques. SID has the advantage that no pump-down delay is needed and, therefore, more cycles of MS/ MS can be completed. 

ESI-Infrared Multiphoton Dissociation IRMPD of ESI-generated ions can also provide sequence information. By combining the data from the nozzle-skimmer dissociation and IRMPD experiments, nearly complete sequence coverage for larger oligonucleotides can be obtained [48]. These two dissociation techniques yield complementary sequence ions. For example, IRMPD primarily produces w- and (a — B )-type sequence ions, whereas the nozzle-skimmer dissociation generates b-, c-, and [Pg.467]

Several gas-phase fragmentation techniques have found a niche as a possible means to sequence oligonucleotides. These include ESI in-source CID (nozzle-skimmer voltage to induce fragmentation), IRMPD in an FT-ICR MS instrument, MALDI in-source decay and post-source decay, and CID-MS/MS of the ESI-produced ions. CID generates complementary (a — B )- and in-type ions, which can provide bidirectional sequencing from the 5 3 direction and 3 5 ... 

Activation of the vibrational energy of ions can also be induced by the absorption of IR radiations. A popular type of IR radiation source is far-IR laser. In fact, many molecules have a broad IR absorption band. The most widely used IR source is a continuous wave (c.w.) CO2 laser, with the wavelength of 10.6 pm. This wavelength corresponds to an energy of 0.3 eV per laser photon. Because decomposition of a chemical bond requires >1 eV, laser excitation has to extended over hundreds of milliseconds to allow ions to absorb multiple IR photons. This method is known as infrared multiphoton dissociation (IRMPD). Another type of similar technique is black-body infrared radiative dissociation... 

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